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Related Concept Videos

Cis-regulatory Sequences02:02

Cis-regulatory Sequences

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Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
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Overview of Transposition and Recombination02:13

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Transposons make up a significant part of genomes of various organisms. Therefore, it is believed that transposition played a major evolutionary role in speciation by changing genome sizes and modifying gene expression patterns. For example, in bacteria, transposition can lead to conferring antibiotic resistance. Movement of transposable elements within the genetic pool of pathogenic bacteria can aid in transfer of antibiotic-resistant genetic elements. In eukaryotes, transposons can carry out...
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Transcriptional regulators bind to specific cis-regulatory sequences in the DNA to regulate gene transcription. These cis-regulatory sequences are very short, usually less than ten nucleotide pairs in length. The short length means that there is a high probability of the exact same sequence randomly occurring throughout the genome.  Since regulators can also bind to groups of similar sequences, this further increases the chances of random binding. Transcriptional regulators form...
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Master Transcription Regulators02:23

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Master transcription regulators are regulatory proteins that are predominantly responsible for regulating the expression of multiple genes. Often these genes work in concert to drive a  complex process. Activation of a master transcription regulator can lead to a cascade of transcriptional activation necessary for that outcome. These regulators can directly bind to the regulatory sequences of the various genes involved, or they can indirectly regulate transcription by binding to regulatory...
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Lateral Root Inducible System in Arabidopsis and Maize
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Widespread long-range cis-regulatory elements in the maize genome.

William A Ricci1, Zefu Lu2, Lexiang Ji3

  • 1Department of Plant Biology, University of Georgia, Athens, GA, USA.

Nature Plants
|November 20, 2019
PubMed
Summary

Gene-distal loci in maize act as long-range cis-regulatory elements controlling gene expression. This study provides genetic and functional evidence for these widespread regulatory elements, enhancing our understanding of crop trait control.

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Area of Science:

  • Plant genetics and genomics
  • Molecular biology
  • Epigenetics

Background:

  • Agronomic traits in crops can be influenced by gene-distant intergenic regions.
  • These gene-distal loci are largely uncharacterized despite their biological significance and potential for crop improvement.

Purpose of the Study:

  • To investigate the existence and function of gene-distal loci as long-range transcriptional cis-regulatory elements (CREs) in the maize genome.
  • To provide genetic, epigenomic, and functional evidence for these regulatory elements.

Main Methods:

  • Analysis of genetic mapping data in crops.
  • Epigenomic profiling to identify euchromatic features.
  • Chromatin conformation capture to identify DNA loops.
  • Self-transcribing active regulatory region sequencing (STARR-seq) to measure enhancer activity.

Main Results:

  • Gene-distal loci in maize are enriched for features indicative of regulatory function.
  • Chromatin looping connects putative CREs with target genes, consistent with genetic interactions.
  • Putative CREs exhibit significant transcriptional enhancer activity.

Conclusions:

  • The study provides strong evidence for the widespread presence and function of gene-distal cis-regulatory elements in maize.
  • These elements regulate gene expression over long genomic distances, offering new targets for crop improvement.